biolockj.module.implicit.parser.r16s

Class RdpParser

java.lang.Object

biolockj.module.BioModuleImpl

biolockj.module.ScriptModuleImpl

biolockj.module.JavaModuleImpl

biolockj.module.implicit.parser.ParserModuleImpl

biolockj.module.implicit.parser.r16s.RdpParser

All Implemented Interfaces:

BioModule, ParserModule, JavaModule, ScriptModule, Comparable<BioModule>

public class RdpParser
extends ParserModuleImpl

This BioModule parses RDP output files to build standard OTU abundance tables.

GUI Module Name

RDP Parser

Field Summary

Fields inherited from class biolockj.module.implicit.parser.ParserModuleImpl

NUM_OTUS

Fields inherited from class biolockj.module.JavaModuleImpl

BLJ_OPTIONS

Fields inherited from class biolockj.module.BioModuleImpl

GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT

Fields inherited from interface biolockj.module.ScriptModule

SCRIPT_BATCH_SIZE, SCRIPT_DEFAULT_HEADER, SCRIPT_NUM_THREADS, SCRIPT_PERMISSIONS, SCRIPT_TIMEOUT

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Constructor Summary

Constructors

Constructor and Description
RdpParser()

Method Summary

Modifier and Type	Method and Description
protected boolean	isValid(OtuNode node) If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.
void	parseSamples() Parse all RdpClassifier reports in the input directory. Build an RdpNode for each line. If isValid(OtuNode), Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

Methods inherited from class biolockj.module.implicit.parser.ParserModuleImpl

addOtuNode, buildOtuCountFiles, checkDependencies, getDepricatedOtuCountFields, getOtuCountField, getParsedSample, getSummary, runModule, setNumHitsFieldName, validateModuleOrder

Methods inherited from class biolockj.module.JavaModuleImpl

buildScript, executeTask, getSource, getWorkerScriptFunctions, isValidInputModule, markStatus, moduleComplete, moduleFailed

Methods inherited from class biolockj.module.ScriptModuleImpl

buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getTimeout, hasScripts

Methods inherited from class biolockj.module.BioModuleImpl

cacheInputFiles, cleanUp, compareTo, equals, findModuleInputFiles, getFileCache, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, toString, validateFileNameUnique

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface biolockj.module.JavaModule

moduleComplete, moduleFailed

Methods inherited from interface biolockj.module.ScriptModule

buildScript, buildScriptForPairedReads, getJobParams, getMainScript, getScriptDir, getScriptErrors, getTimeout, getWorkerScriptFunctions

Methods inherited from interface biolockj.module.BioModule

cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getTempDir, init, isValidInputModule

Constructor Detail

RdpParser

public RdpParser()

Method Detail

parseSamples

public void parseSamples()
                  throws Exception

Parse all RdpClassifier reports in the input directory.
Build an RdpNode for each line.
If isValid(OtuNode),

1. Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
2. Add the OtuNodeImpl.getCount() (1) to ParsedSample OTU count.

Sample QIIME report line (head 7A_1_reported.tsv):
FCABK7W:1:2105:21787:12788#/1 Root rootrank 1.0 Bacteria domain 1.0 Firmicutes phylum 1.0 Clostridia class 1.0 Clostridiales order 1.0 Ruminococcaceae family 1.0 Faecalibacterium genus 1.0

Specified by:

parseSamples in interface ParserModule

Specified by:

parseSamples in class ParserModuleImpl

Throws:

Exception - if error occurs while parsing classifier reports

isValid

protected boolean isValid(OtuNode node)

If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.

Overrides:

isValid in class ParserModuleImpl

Parameters:

node - OtuNode build from 1 line of a ClassifierModule output file

Returns:

true if OtuNode is valid